Homo sapiens sapiens has spread across the globe and increased vastly in numbers over the past 50,000 years or so—from an estimated five million in 9000 B.C. to roughly 6.5 billion today. More people means more opportunity for mutations to creep into the basic human genome and new research confirms that in the past 10,000 years a host of changes to everything from digestion to bones has been taking place.

"We found very many human genes undergoing selection," says anthropologist Gregory Cochran of the University of Utah, a member of the team that analyzed the 3.9 million DNA sequences* showing the most variation. "Most are very recent, so much so that the rate of human evolution over the past few thousand years is far greater than it has been over the past few million years."

"We believe that this can be explained by an increase in the strength of selection as people became agriculturalists—a major ecological change—and a vast increase in the number of favorable mutations as agriculture led to increased population size," he adds.

Roughly 10,000 years ago, humanity made the transition from living off the land to actively raising crops and domesticated animals. Because this concentrated populations, diseases such as malaria, smallpox and tuberculosis, among others, became more virulent. At the same time, the new agriculturally based diet offered its own challenges—including iron deficiency from lack of meat, cavities and, ultimately, shorter stature due to poor nutrition, says anthropologist John Hawks of the University of Wisconsin–Madison, another team member.

"Their bodies and teeth shrank. Their brains shrank, too," he adds. "But they started to get new alleles [alternative gene forms] that helped them digest the food more efficiently. New protective alleles allowed a fraction of people to survive the dread illnesses better."

By looking for wide swaths of genetic material that vary little from individual to individual within these sections of great variation, the researchers identified regions that both originated recently and conferred some kind of advantage (because they became common rapidly). For example, the gene known as LCT gave adults the ability to digest milk and G6PD offered some protection against the malaria caused by Plasmodium falciparum parasite.

"Ten thousand years ago, no one on planet Earth had blue eyes," Hawks notes, because that gene—OCA2—had not yet developed. "We are different from people who lived only 400 generations ago in ways that are very obvious; that you can see with your eyes."

Comparing the amount of genetic differentiation between humans and our closest relatives, chimpanzees, suggests that the pace of change has accelerated to 10 to 100 times the average long-term rate, the researchers write in Proceedings of the National Academy of Sciences USA.

Not all populations show the same evolutionary speed. For example, Africans show a slightly lower mutation rate. "Africans haven't had to adapt to a fundamentally new climate," because modern humanity evolved where they live, Cochran says. "Europeans and East Asians, living in environments very different from those of their African ancestors and early adopters of agriculture, were more maladapted, less fitted to their environments."

And this speedy pace of evolution will not slow until every possible beneficial mutation starts to happen—the maximum rate of adaptation. This has already begun to occur in such areas as skin color in which different sets of genes are responsible for the paler shades of Europeans and East Asians, according to the researchers.

The finding raises many questions. Among them: "the medical applications of this kind of knowledge [as well as] exactly what most of the selected changes do and what drove their selection," Cochran says.

But the history of humanity is beginning to be read out from our genes, thanks to a detailed knowledge of the thousands of them that have evolved recently. "We're going to be classifying these by functional categories and looking for matches between genetic changes and historic and archaeological changes in diet, skeletal form, disease and many other things," Hawks says. "We think we will be able to find some of the genetic changes that drove human population growth and migrations—the broad causes of human history."

*This article wrongly characterized the HapMap genotype dataset used for this analysis as "genes" rather than "DNA sequences."